Fox Mulder at the airport, 1997: flashes his badge and gets a private escort to a different terminal. Metal detector goes off when he passes through it while carrying two pistols and talking on his cell phone? No problem, flashes his badge and the airport guy lets him take a peek at his X-ray. (The X-Files, Season 4, episode 18: Max)

Olivia Dunham at the airport, 2012: Tries to stop bad guy, gets stopped by TSA. Flashes her badge, is a terrorist.

Whoever wrote the script clearly had a bad experience at an airport, making TSA a secondary antagonist

When Peter came back, he was thrust into yet another universe, this episode pretty much confirmed that it's a 3rd universe with everything that was occuring.
Then the alt universe that exists in this universe is a 4th universe.
Yes, it can get a bit confusing with all of these universes but that's how alternate realities would work if they existed.

I disagree, I believe there are 5 - not 4.
Universe/Timeline 1 is the 'main universe' and is from season one.
Universe/Timeline 2 was featured heavily in season 2 and three.
Universe/Timeline 3 is created when Peter creates a bridge between Universes 1 and 2, merging them together at the end of season three and pushing him out of existence.
Universe/Timeline 4 is the one that Peter is thrown into, being the main focus of season 4.
Universe/Timeline 5 is the alternate version of 4. (the universe where Walternate is actually good)

Okay so then technically there's still only 4 universes since the Retro scenes count towards our universe.
Though, you could probably discount the future too since I doubt that's going to be making a come back.